Moses Okpeku

Morphological and microsatellite DNA diversity of Nigerian indigenous sheep

BackgroundSheep is important in the socio-economic lives of people around the world. It is estimated that more than half of our once common livestock breeds are now endangered. Since genetic characterization of Nigerian sheep is still lacking, we analyzed ten morphological traits on 402 animals and 15 microsatellite DNA markers in 384 animals of the 4 Nigerian sheep breeds to better understand genetic diversity for breeding management and germplasm conservation.ResultsMorphological traits of Uda and Balami were significantly (P < 0.05) higher than Yankasa, which were both higher than West African Dwarf (WAD) sheep. Stepwise discriminant analysis showed tail length, rump height, chest girth, ear length and chest depth as the most discriminating variables for classification. Mahalanobis distances show the least differentiation between Uda and Balami and the largest between WAD and Balami sheep. While 93.3% of WAD sheep were correctly assigned to their source genetic group, 63.9% of Yankasa, 61.2% of Balami and 45.2% of Uda were classified correctly by nearest neighbour discriminant analysis. The overall high Polymorphism Information Content (PIC) of all microsatellite markers ranged from 0.751 to 0.927 supporting their use in genetic characterization. Expected heterozygosity was high for all loci (0.783 to 0.93). Mean heterozygote deficiency across all populations (0.171 to 0.534) possibly indicate significant inbreeding (P < 0.05). Mean values for FST, FIT and FIS statistics across all loci were 0.088, 0.394 and 0.336 respectively. Yankasa and Balami are the most closely related breeds (DA = 0.184) while WAD and Balami are the farthest apart breeds (DA = 0.665), which is coincident with distance based on morphological analysis and population structure assessed by STRUCTURE.ConclusionsThese results suggest that within-breed genetic variation in Nigerian sheep is higher than between-breeds and may be a valuable tool for genetic improvement and conservation. The higher genetic variability in Yankasa suggests the presence of unique ancestral alleles reflecting the presence of certain functional genes which may result in better adaptability in more agro-ecological zones of Nigeria. These genetic characteristics are potentially useful in planning improvement and conservation strategies in Nigerian indigenous sheep.

Genetic diversity analysis of the mitochondrial D-loop of Nigerian indigenous sheep

Los recursos ganaderos autoctonos son de caracter estrategico en los aspectos socioeconomicos de los sistemas agricolas para garantizar la seguridad alimentaria en los paises de escasos recursos. Por lo tanto, conocer mejor la importancia de la variabilidad genetica es vital para su futura utilizacion, por medio de la conservacion. Se presenta el primer analisis de la diversidad genetica en ovejas de Nigeria basado en la region de control (D-loop) del Ovis aries del genoma mitocondrial, utilizando 1.179 bases entre las posiciones 15.437 y 16.616 de pares de bases. Una muestra de 290 animales, compuesta por las razas Balami, West African Dwarf (WAD), Uda y Yankasa, fue tomada al azar de toda Nigeria. Se observaron noventa y seis (96) haplotipos, con una alta diversidad media en cuanto a estos de 0,899 ± 0,148. La diversidad genetica fue mayor en la raza Uda (0,921 ± 0,021) y menor en la raza WAD (0,852 ± 0,061). Los indices de poblacion especificos FST variaron de 0.00133 en la raza Uda a 0,00335 en la razaWAD. La raza Yankasa presento el mayor numero de posiciones polimorficas (201), mientras que el menor lo mostro la raza Uda (96). Analisis de la varianza molecular revelo que 0,23% de la variacion se encuentra entre las poblaciones, en comparacion con el 99,77% de variacion que se encuentra dentro de las poblaciones. El arbol filogenetico indica que los linajes mitocondriales de las razas ovinas partieron de un origen comun en conformidad con la primera divergencia de la raza Yankasa, seguida por WAD, mientras que las razas Balami y Uda se encuentran mas estrechamente relacionadas. Estos resultados demuestran que la divergencia evolutiva de las poblaciones ovinas de Nigeria, basados en el ADN mitocondrial de la region control, puede coincidir con la distribucion geografica en Nigeria e indican una tasa importante de cruzamiento entre ellas. Esto podria tener ventajas desde el punto de vista de la gestion de la mejora y las estrategias de conservacion y preservacion a largo plazo de las ovejas autoctonas de Nigeria.

Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats

Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats. Fourteen different types of alleles identified in the Nigerian goats, four of which were found in the peptide coding region (A57G, Q89R, G104D, and T112I), indicate a high degree of polymorphism at the DRB locus in this species. An obvious excess (P < 0.01) of non-synonymous substitutions than synonymous (dN/dS) in this locus is a reflection of adaptive evolution and positive selection. The phylogenetic trees revealed largely species-wise clustering in DRB gene. BsaHI, AluI, HaeIII, and SacII genotype frequencies were in Hardy-Weinberg equilibrium (P > 0.05), except AluI in RS goats and HaeIII in WAD goats (P < 0.05). The expected heterozygosity (H), which is a measure of gene diversity in the goat populations, ranged from 0.16 to 0.50. Genotypes AA (BsaHI), GG, GC and CC (AluI) and GG, GA, AA (HaeIII) appeared better in terms of heat tolerance. The heat-tolerant ability of SH and RS goats to the hot and humid tropical environment of Nigeria seemed better than that of the WAD goats. Sex effect (P < 0.05) was mainly on pulse rate and heat stress index, while there were varying interaction effects on heat tolerance. Variation at the DRB locus may prove to be important in possible selection and breeding for genetic resistance to heat stress in the tropics.

Genetic Variation of Goat Interferon Regulatory Factor 3 Gene and Its Implication in Goat Evolution

The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats’ populations. Fu and Li tests were significantly positive but Tajima’s D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of IRF3 gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model dN/dS ratio for all goats was greater than one. Phylogenetic Analysis by Maximum Likelihood (PAML) gave a ω0 (dN/dS) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in IRF3 gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution may have been influenced by domestication processes in goats.

Mitochondrial DNA hypervariable region 1 diversity in Nigerian goats – CORRIGENDUM

Moses Okpeku, Sunday O. Peters, Ikhide G. Imumorin, Kyle C. Caires, Varun K. Sharma, Mathew Wheto, Rakesh Tamang, Adeyemi S. Adenaike, Michael O. Ozoje and Kumarasamy Thangaraj doi: 10.1017/S2078633616000102, Published by Cambridge University Press, 3 January 2017 In the above publication (Okpeku, 2017) the incorrect affiliation was given for Kyle Caires. The correct affiliation is: Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaì i at M anoa, Honolulu, HI 96822, USA

Mitochondrial DNA hypervariable region 1 diversity in Nigerian goats

espanolLas cabras constituyen el mayor grupo de ganado rumiante en Nigeria y desempenan un papel estrategico en el aporte de proteina animal y en la mejora de la economia de los hogares rurales. Se investigo acerca de la region hipervariable 1 (HVR1) del genoma mitocondrial caprino con el fin de comprender mejor la importancia de la diversidad genetica para mejorar la seleccion en los programas de mejora y conservacion animal. Se secuencio y se analizo la region hipervariable 1 del ADN mitocondrial (HVR1) en 291 cabras autoctonas de Nigeria no relacionadas (Enana de Africa Occidental (EAO), Roja de Sokoto (RS) y Sahel (S)), seleccionadas aleatoriamente a lo largo del pais y comparadas con las secuencias HVR1 de 336 cabras indias y con otras 12 secuencias de 5 especies diferentes del generoCapra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis yC. sibirica). Un total de 139 sitios polimorficos de 291 individuos se concentraron en 204 haplotipos. La variacion intra- e interpoblacional fue de 77,25 por ciento y de 22,74 por ciento, respectivamente. Las cabras nigerianas mostraron una elevada diversidad genetica (0,87) y unos valores de FST elevados, distintos de los de las cabras indias y de los de las otras especies salvajes. De acuerdo con los haplogrupos, la cabra EAO se desliga de poblaciones concomitantes de RS y S con una historia demografica diferente. Se identifico una estructura genetica clara entre las razas caprinas de Nigeria, con una variacion apreciable en la region HVR1 del ADN mitocondrial. Este estudio agrupo las razas caprinas nigerianas en dos grupos principales, sugiriendo asi dos origenes demograficos distintos para las razas septentrionales y meridionales. El alto grado de mezcla genetica denota origenes maternos distintos, a diferencia de lo observado en cabras del Levante y Asia Central, donde se domesticaron originalmente las cabras. Palabras clave: diversidad genetica, cabras, region hipervariable, ADN mitocondrial, Nigeria EnglishGoats make up the largest group of ruminant livestock in Nigeria and are strategic in bridging animal protein supply gap and improving the economy of rural households. The hypervariable region 1 (HVR1) of the caprine mitochondrial genome was investigated to better understand genetic diversity important for improving selection for animal breeding and conservation programs. We sequenced and analysed the mitochondrial DNA (mtDNA) HVR1 in 291 unrelated indigenous Nigerian goats (West African Dwarf (WAD), Red Sokoto (RSO) and Sahel (SAH)), randomly sampled from around the country, and compared them with the HVR1 sequences of 336 Indian goats and 12 other sequences in five different species in the genusCapra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis andC. sibirica). A total of 139 polymorphic sites from 291 individuals were captured in 204 haplotypes. Within and among population variations were 77.25 and 22.74 percent, respectively. Nigerian goats showed high genetic diversity (0.87) and high FST values, and separate from Indian goats and other wild species. Haplogroups in WAD separates it from RSO and SAH concomitant with a differentdemographic history. Clear genetic structure was found among Nigerian goat breeds with appreciable variation in mtDNA HVR1 region. This study grouped Nigerian goat breeds into two major groups suggesting two different demographic origins for Northern and Southern breeds. High genetic admixing denotes different maternal origins and in contrast to evidence from goats from Levant and Central Asia, where goats were originally domesticated. Keywords: genetic diversity, goats, hypervariable region, mitochondrial DNA, Nigeria francaisLes caprins constituent le plus grand groupe de ruminants domestiques au Nigeria et jouent un role strategique dans l’approvisionnement en proteines animales et dans l’amelioration de l’economie des menages ruraux. Une recherche a ete menee a propos de la region hypervariable 1 (HVR1) du genome mitochondrial caprin dans le but de mieux comprendre l’importance de la diversite genetique pour ameliorer la selection dans les programmes d’amelioration genetique et de conservation des animaux. La region hypervariable 1 de l’ADN mitochondrial (HVR1) a ete sequencee et analysee chez 291 chevres indigenes du Nigeria, sans rapport entre elles (Naine d’Afrique Occidentale (NAO), Rouge de Sokoto (RS) et Sahel (S)), echantillonnees de maniere aleatoire a travers le pays et comparees avec les sequences HVR1 de 336 chevres indiennes et avec 12 autres sequences de 5 especes differentes du genre Capra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis et C. sibirica). Un total de 139 sites polymorphes de 291 individus a ete rassemble en 204 haplotypes. La variation intra- et inter-populationnelle a ete de 77,25 pour cent et de 22,74 pour cent, respectivement. Les caprins nigerians ont montre une grande diversite genetique (0,87) et des valeurs de FST elevees et differentes de celles des chevres indiennes et de celles des autres especes sauvages. D’apres les haplogroupes, la chevre NAO serait a separer des populations concomitantes de RS et S avec une histoire demographique differente. Une structure genetique claire a ete decelee entre les races caprines du Nigeria, avec une variation substantielle dans la region HVR1 de l’ADN mitochondrial. Cette etude a regroupe les races caprines nigerianes en deux groupes principaux, ce qui suggere deux origines demographiques differentes pour les races du Nord et du Sud. Le fort degre de melange genetique denote des origines maternelles differentes, contrairement a ce qui a ete observe chez les chevres du Levant et d’Asie Centrale, ou les caprins furent d’abord domestiques. Mots-cles: diversite genetique, caprins, region hypervariable, ADN mitochondrial, Nigeria